is the Director of Vital-IT Group in Lausanne as well as the Swiss-Prot Group in Geneva. He received a Ph.D in immunology at the Ludwig Institute of Cancer Research and the Institute of Biochemistry. He worked on the development of the Database of Interacting Proteins (DIP) under the supervision of Prof. David Eisenberg at the University of California Los Angeles. He then became the head of Translational Bioinformatics at Serono (now Merck Serono) where his group developed computational methodologies in the area of proteomics, microarray and genetics. He is one of the Principal investigators of the ENFIN project aiming at providing methods in dynamical systems modeling. Ioannis Xenarios is UNIL full Professor ad personam, affiliated with the CIG, since August 2010
studied Biology at the university of Lausanne. She obtained a master degree in Molecular Life Sciences with a distinction in Bioinformatics at the university of Lausanne in 2015. For her Master's degree project, she joined Vital-IT and worked on modeling and simulation of the underlying regulatory network of epithelial-to-mesenchymal transition in cancer. She joined Vital-IT as PhD student in 2015
studied Biology at Université de Lausanne, where he obtained his Master in Biology. He also obtained a Licence es Sciences with subjects Informatics and Biology. After a musical parenthesis, he worked at BCF-SIB on prediction of Coiled coil domains, using HMM and MAMOT. In parallel, he worked on several projects as a web developer. He then worked at CHUV, in collaboration with Vital-IT on enzymatic pathways and gene prediction in Pneumocystis spp. In 2009, he joined the Stratified Medicine research group at Merck Serono in Geneva, working on biomarkers discovery. In 2012, he joined the Vital-IT group where he is involved in analysis of genomics and proteomics data for the IMIDIA project and various other research projects.
After seven years as professor at the University of Lausanne (New Testament and Digital Humanities), Claire Clivaz is now Head of Digital Enhanced Learning at the SIB. She leads her researches in an interdisciplinary way, at the crossroad of New Testament and the digital transformations of knowledge, as her bibliography shows it (https://isb-sib.academia.edu/ClaireClivaz/). She leads the development of the etalks, a multimedia publication tool (etalk.vital-it.ch), as well as a Swiss National Fund on the Arabic manuscripts of Pauline letters (wp.unil.ch/nt-arabe/) and participates with six other European partners to a strategic partenariat ERASMUS+ in Digital Humanities (dariah.eu/teach). She is a member of several scientific committees (ADHO steering committee, EADH steering committee, IGNTP, Humanistica, etc.) and editorial boards (NTS, Digital Religion de Gruyter, etc.). She is co-leading a series with David Hamidovic by Brill «Digital Biblical Studies», and research groups in DH (SBL, EABS).
studied veterinary followed by a Master in Bioinformatics and Computational Biology at Universidad Complutense de Madrid. As a PhD student at Luxembourg Centre for Systems Biomedicine, he worked on disease description and cellular reprogramming using Systems Biology and Computational Biology approaches. In December 2013, he joined Vital-IT where he is working in the development of new methods for tumor microenvironment modelling.
studied neurobiology at Paris-6 University, where he obtained a Master’s degree in neurosciences in 1984. As PhD student at Collège de France, he worked on the functional development of the visual system using electrophysiological exploration, and initiated computational approaches to model and integrate experimental data. He completed his education in computer science with a Master’s degree in “Image and Artificial Intelligence” obtained from Sup’ Telecom in 1991, and then joined Thomson-CSF (now Thales) to develop neural network models for object identification and tracking, and to design neuromorphic electronic devices for smart image sensors. In 1997 he joined the biotech company Genset, later acquired by Serono (now Merck Serono), where he was involved in image/signal interpretation, genomic mining for active peptides, and pharmacogenomics of clinical trials for biomarker discovery. In 2013 he joined the Vital-IT group, where he is involved in analysis of genomics data for the NRP-63 and AgedBrainSYSBIO projects.
studied mathematics and biology at the University of Geneva, then mathematics at Ecole Polytechnique Fédérale de Lausanne (EPFL). He obtained a Master's degree in applied mathematics in 2011, then was employed as a bioinformatician for 4 years at the Bioinformatics and Biostatistics Core Facility, at EPFL. He joined Vital-IT as a developer-analyst, working also half-time for the Lausanne University Hospital (CHUV). His main activity is programming applications for the analysis of genetic variants from sequencing data.
studied theoretical physics at the Swiss Institute of Technology in Lausanne (EPFL). He obtained his diploma in 2004 and a PhD in 2008 in the field of quantum magnetism. He then moved to the University of Lausanne where he worked as Senior FNS researcher, using numerical simulations to study the 3D organization of chromatin fibers in cell nuclei. In 2011 he joined the Vital-IT group.
studied biology with an emphasis on plant ecology and geographical information systems (GIS). Interested in combining spatial analysis, statistical modeling and ecological data, he specialized in the field of species distribution modeling and joined the Spatial Ecology lab at the University of Lausanne, from which he obtained a PhD in 2009. In parallel of his thesis and in the years thereafter, he worked as scientific collaborator specialized in GIS for the Seismic Atlas of the Swiss Molasse Basin, a collaboration between the Swiss Geophysical Commission, the University of Lausanne, and the Swiss federal office of topography. In early 2014 he joined Vital-it to work on spatial epidemiology risk modeling.
took a Master's in Physics at the Swiss Federal Institute of Technology in Zurich in 1987 and then continued to a PhD thesis at CERN in Geneva. In 1993 he became a database developer for the Cardiology Center of the Geneva university hospital, and in 1997 joined the future Swiss Institute of BioInformatics as a systems engineer. From 2000 to 2003 he worked as High Performance Computing manager at GeneProt and led its effort to set up what was at the time the world's most powerful civilian computer farm. He is now the IT manager for Vital-IT.
was raised in France. He then moved to Germany to study Computer Science at the University of Kaiserslautern, followed by the university of Lausanne where he obtained a diploma in Biology in 1998. He also obtained a Masters degree in Bioinformatics in Lausanne in 2001. Immediately after, he started working at the SIB in Dr. Philipp Bucher's group, maintaining the sequence analysis package 'pftools' as well as system administrative tasks on the SIB's Lausanne computer infrastructure. In 2004, he joined the Vital-IT team, working as junior system administrator and software programmer specializing in adapting and optimizing life-science applications for the Vital-IT cluster architecture.
studied biology and computer sciences at the 'Université de la Mediterranée' at Marseille. She obtained a masters degree in proteomics and bioinformatics at the university of Geneva in 2013, and did her master project in glycomics in the PIG group of SIB in Geneva. She joined Vital-IT as a web developer in 2014.
studied plant biology and biochemistry at the University of Lausanne. In the early nineties, during the course of his PhD,
he pioneered the use of molecular biology in the Institute of Plant Biology, isolated and sequenced two genes of the glyoxylate
cycle, built a molecular model for one of them and initiated the development of Swiss-PdbViewer.
He obtained his PhD in 1995 and joined the group of Manuel Peitsch at GlaxoWellcome, where he contributed to the development of
From 1996-2002, he also taught postgrade Structural Biology modules at the University of Geneva, EPFL and for the Swiss Institute of Bioinformatics.
During his 12 years at GlaxoSmithKline, he occupied positions of increasing responsibilities, led a group specialized in Evolutionary and Structural Bioinformatics and contributed to several drug discovery research programs.
Nicolas has been developing and optimizing computer software since 1979, and joined the Vital-IT team in 2008 where he continues the development of Swiss-PdbViewer, contributes his bioinformatics and biology expertise to research groups and develop specialized software to support research projects that necessitate high performance computing.
studied genetics at Nottingham University, UK and obtained a PhD from Imperial College, London on the genetics of the T cell receptor alpha gene locus in 1995. He then moved to Lausanne as a postdoc in the laboratory of Bernard Thorens where he cloned and characterized a new mammalian glucose transporter, GLUT8, and generated double Glp1/Gip receptor knockout mice. In 2000, he joined Serono (now Merck Serono) as a bioinformatician supporting drug discovery projects and developing methodologies for sequence analysis and research knowledge management. In 2010, he joined Vital-IT where he is involved in analysis of genomics and proteomics data for the Imidia project and various other research projects.
studied biology at the University of Lausanne where he obtained, in 1997, his Diploma in virology and molecular oncology and in 2001, his PhD in immunology. He then went on to obtain a Master in Bioinformatics from the Universities of Lausanne and Geneva in 2002. In 2002, he joined the Swiss EMBnet node at the Swiss Institute of Bioinformatics as Bioinformatician where he was responsible for organizing undergraduate and post-graduate courses, and was involved in teaching activities as well. He was also member of the EMBnet Education and Training Project Committee. In addition, he participated in providing help desk support to the life sciences community, which led to a number of collaborations, and was in charge of several web sites. In 2009, he joined the Vital-IT group where he continues these activities and is now a member of the SIB web-team.
has obtained a CFC (professional certificate) in agriculture followed by a Master’s degree in computer engineering from EPFL and Carnegie Mellon University. He then obtained a Ph.D. from EPFL with focus on a high performance reconfigurable processor and its software development environment. He started his professional career with activities in both academia (Systems Manager at ISREC) and industry (software developer at Xemics SA). In 1998 he joined the Ludwig Institute for Cancer Research as Systems Manager (Office of Information Technology) and subsequently as Assistant Investigator in the Computational Genomics group and finally as project manager for the Melanoma sequencing project. In 2011 he joined the Vital-IT Group as Senior Scientist.
studied biology at Madurai Kamaraj University (India) with emphasis on bacterial genetics and also obtained her diploma in Bioinformatics from the same university. She then went on to obtain her Ph.D. in Bioinformatics from the University of Lausanne in 2007. She worked as a post-doc also in the University of Lausanne before joining Vital-IT in Feb 2011.
is a physical chemist with a M.Sc. in chemical engineering and a Ph.D. in biophysical chemistry. In the summer of 2009 she joined the Swiss Institute of Bioinformatics where she is involved in the development of new methods for protein modelling.
studied biology at the University of Lausanne, with emphases in plant systematics and mathematics, and got a diploma in microbiology from the same university. He also worked as a bioinformatician for a small start-up company. He joined Vital-IT in 2011 after completing a PhD in high-throughput phylogenomics of vertebrates and viruses with E. Zdobnov at the University of Geneva.
educated at Moscow State University as a physico-chemist in 1982. During the next 15 years, he was working at the Institute of Molecular Biology (Russia) doing both experimental assays (enzymatic kinetics and NMR) and modelling of protein structures. He obtained his PhD in biophysics on structure modelling of MHC-TCR protein complex in collaboration with the Ludwig Institute of Cancer Research (LICR) in Lausanne. He spent the next 8 years in Lausanne working for the LICR as a database administrator (DBA) and web developer in various bioinformatic projects. After joining the Vital-IT team in 2007, he continues to work as a DBA and developer on the MySQL and Oracle platform.
After obtaining his Ecomomy & Law high-school degree, Leonardo Ledesma S. decided to go to the "Gymnase" for a degree in Federal Ecomomy & Law. Upon graduation, he applied to SIB for one year, as part of his training programme for the "Maturité professionnelle Commerciale". In September 2014, he joined SIB where his main tasks were distributed between the Finances department and the Vital-IT group's secretariat. Following this year, he decided to remain at SIB while pursuing his studies at the "HEIG". Leonardo Ledesma S.
studied plant biology at the University of Lausanne where he obtained his diploma in 1999. He then obtained a master in bioinformatics from the Universities of Lausanne and Geneva in 2001. In 2005, he obtained his PhD on signaling pathways leading to plant defense by combining gene expression, proteomics and bioinformatics analyses. Since 2006 he is working at Vital-IT for the EuroDia european project on type 2 diabetes. He is developing a web-based relational database to store, annotate, combine and analyze gene expression data obtained with various technologies and different model organisms. This system offers user-friendly web interface to several bioconductor statistical packages. Robin is also involved in setting up openfludb, a database to share Influenza genetical and epidemiological data.
holds a PhD in Biostatistics from the University of Lausanne (2010). She started studying biology and then took an interest in Bioinformatics and Biostatistics for which she got a Master degree at the University of Paris XI (2005). During her PhD and her Post-doc at the Department of Medical Genetics (UNIL-CHUV/SIB), she mainly worked on the pharmacogenetics study of the Swiss HIV cohort data and on Genome-Wide Association Studies (GWAS) on human phenotypic traits. She joined the Vital-IT group in April 2013 to analyze and follow-up various research projects and to take an active part in the SIB Education coordinating team.
studied Biology at the University of Lausanne where he obtained his Diploma in 2001. A year later he obtained a Master in Bioinformatics at the Universities of Geneva and Lausanne. He then worked in the field of web/software development for several years, mainly specializing into Java programming language. In 2006 he joined the Swiss Institute of Bioinformatics and quickly after that, Vital-IT team, as a bioinformatician/software developer. He has been involved since in the development of AssociationViewer, a flexible and scalable application for visualization of large-scale genomic data.
studied Computer Science Engineering followed by a Master in Software Engineering at Universidad Complutense de Madrid. In 2013 she received a second Master diploma in Bioinformatics and Computational Biology at National School of Health, Madrid. As a master student at Luxembourg Centre for Systems Biomedicine Trinidad worked on cellular reprogramming using Systems Biology and Computational Biology approaches. In November 2013 she joined Vital-IT where she is working as Bioinformatician.
holds a degree in foreign languages (English, Italian and German) and a Diploma of Executive Secretary. She also studied one year psychology at the University of Lausanne. She worked for several years in trust companies as secretary, before to join the Vital-IT team in 2007 and assist Prof Ioannis Xenarios.
obtained his Master's degree in Telecommunications at UPV in Spain after completing the MSc final project at the Technical University of Munich, then expanded his education at the University of Waterloo. He started his professional experience at the European Space Agency and the European Commission before arriving at CERN, where he worked for its two main experiments: first in ATLAS as software developer and then in CMS as responsible of a computer cluster. Since 2014 Jorge is part of the Vital-IT system administration team.
studied biology at the University of Lyon where he obtained, in 1999, his Diploma in Population Biology and Ecosystems.
He then went on to obtain a Master in Population Biology, Genetics and Eco- ethology (with a specialisation in Entomology)
from the University of Tours. A year later he obtained a Master in Bioinformatics from the University of Paris 7.
In 2002, he joined the Genoplante consortium to cluster and annotate Sunflower ESTs, in Toulouse. In 2003, he joined the Genomic and Structural Information lab. (CNRS) in Marseilles, in collaboration with the Aventis pharmaceutical group, to work on Kinase proteins and on Multiple Sequence Alignments tools. Then, in 2006, he joined the Swiss EMBnet node at the Swiss Institute of Bioinformatics and the Department of Ecology & Evolution (DEE) in Lausanne, as Bioinformatician. Since, for EMBnet, he is developing tools for the MyHits web server, maintaining and adding tools for our Soaplab-based Web Services. For the DEE, he is developing Selectome, a database of Positive Selection, Bgee, a database for Gene Expression Evolution, as well as doing system administration.
In 2009, he joined the Vital-IT group where he continues these activities and is now a member of the SIB web-team.
studied Biology at the ETH Zurich from where he obtained a Master’s degree. He continued with a second Master’s and a Ph.D. in Bioinformatics from the University of Geneva. During his Ph.D. he worked on the identification of small molecules by LC-MSMS in a joint project between Geneva Bioinformatics, the SIB Swiss Institute of Bioinformatics and the University Hospital of Geneva. Afterwards he worked at Atheris Laboratories on the analysis of RNA sequences from venomous animals and at Fondazione Edmund Mach on Metabolomics. He joined Vital-IT in 2014 where he works mainly on projects related to Proteomics and mass spectrometry.
studied zoology at the University of Bern and obtained a PhD in population genetics in 2006. The aim of the PhD thesis was to reconstruct the demographic history of freshwater fishes in Switzerland. For this purpose he developed a numerical simulation model allowing simulating the demography of populations and species over time in a realistic spatially explicit environment. He used high throughput computation technics to perform simulations and estimate corresponding demographic and genetic parameters. At the same time he acquired a minor in informatics. He then moved to the University of Lausanne and worked there as a postdoc developing numerical simulation tools in the area of population and quantitative genetics. In 2011 he then joined the Vital-IT group.
studied Biology at the University of Geneva before obtaining a Master degree. She worked many years as biocurator in proteomic area, successively in GeneProt Inc, Meyrin, Switzerland, then in GeneBio, Geneva, Switzerland, as product specialist for an MS/MS identification software (Phenyx), before joining Vital-IT in January 2010, where she works as embedded annotator on various projects.
studied biology at the University of Neuchâtel and obtained a PhD in microbiology. In 1998, he joined the
newly created Swiss Institute of Bioinformatics and has since collaborated with several groups on topics related to sequence
analysis, sequence automated annotation, database design and management and large-scale computation. He joined the Vital-IT
team in 2005, with responsibility for the maintenance and development of the MyHits web server and associated database.
Marco Pagni was also a partner of the EMBRACE European funded project.
holds a joint Master's Degree in Proteomics and Bioinformatics (2009) from the University of Geneva (UNIGE) and the Swiss Institute of Bioinformatics (SIB), and a joint DEA in Information Systems (2006) from UNIGE and Ecole Polytechnique Fédérale de Lausanne (EPFL). She previously developed web-based resources and interactive applications including e-learning modules. In 2008, for her Master's degree project, she joined Protein Analysis Facility at the Center of Integrative Genomics of the University of Lausanne (UNIL). At the end of 2009, she joined Vital-IT team as a Bioinformatician. She is involved in genome annotation and assembly projects in collaboration with the group of Prof. Keller, Department of Ecology and Evolution (DEE), UNIL.
holds a PhD in archaeology from the University of Lyon 2 addressing Late Antique settlement history and land use patterns in margin areas of the Fertile Crescent. Former fellow researcher of the French Institute for the Near East, she worked as a contractual researcher at the French National Center for Scientific Research on cultural heritage databases. The intensive use of geographic information systems and databases led her to become involved in digital humanities. The University of Lausanne recruited her in February 2014 for a pilot-project aiming at ensuring long-term archiving and accessibility of primary research data in humanities. At the same time, she also joined the Vital-IT group in February 2015 as an embedded curator for humanities.
studied Biology at the University of Lausanne and obtained a Master (UV-induced apoptosis, 1996) and a PhD (new family of amino acid transporters, 2000) at the Swiss Institute for Experimental Cancer Research (ISREC). Following a Master in Bioinformatics, he joined GeneBio SA, Geneva in 2001, where he was mainly involved in bioinformatics training (development of an e-learning platform) and as product specialist for Melanie, a software for 2-DE gel image analysis. Since 2006, he has been a member of the SIB. In the Proteome Informatics group, he was involved in e-learning, whereas in the virtual ExPASy group he was in charge of the helpdesk for resources in Proteomics and became member of the Web-Team. In June 2011, he joined Web-Team/Vital-IT. He is currently involved in e-learning, helpdesk for proteomic resources, World-2D PAGE repository and Bioinformatics Core Facility for Proteomics (analysis of 2-DE gel images).
studied biology and computer science at University Paris VII. He obtained his master in Proteomics and Bioinformatics at University of Geneva in 2007 and was enrolled in Genebio S.A, a software solution company for proteomics-based biomedical application. He joined the IGBMC in Strasbourg in 2009 as data scientist in cancer genomics. He then obtained a Ph.D in Lausanne with emphasis on the explanation of various plant morphogenetic phenomena, through data analysis and mathematical modeling. In December 2014, he joined Vital-IT to work on MegaClust analytic service and in Digital Humanities projects.
was trained inBiophysics at Humboldt Universität zu Berlin (DE, 2008) and in Complex Adaptive Systems at Gothenburg University and Chalmers University of Technology (SE, 2010). She received a Ph.D for her work on the evolution of sequence tandem repeats with Maria Anisimova and Olivier Gascuel under the supervision of Sebastian Bonhoeffer from ETH Zürich (CH, 2014). (More information on Elke's CV.) Currently, she is involved with the large scale annotation of genomic tandem repeats, as well as semantic web applications in biological databases.
studied biology at the University Erlangen-Nuernberg in Germany where he
obtained in 2008 his Diploma in biology. He moved afterwards to Lausanne
to study molecular plant biology at the University of Lausanne and
received his PhD in April 213. In August 2013 he joined Vital-IT as a
Post-doc with the goal to serve as an interface between the plant
community and Vital-IT.
is a Physics engineer. He studied at the Swiss Institute of Technology in Lausanne and obtained his diploma in theoretical Physics in 2001 on Random matrices. He then worked on a PhD Thesis applying High Performance Computing in the field of Quantum Chaos. During his studies, he also worked as a part-time software programmer and system administrator for several small businesses.
studied Theology at the University of Lausanne and University of Tübingen (year exchange at the Evangelisch-theologische Fakultät, Eberhard Karls Universität, 2009-2010) and graduated in 2011 (Master of Theology). She completed a research year at the Saint Joseph University (Beirut, 2011-2012). Her thesis focuses on the Arabic manuscripts of the letters of Paul of Tarsus (Swiss National Fund project): cataloguing of manuscripts, edition and analysis of the role of the digital era and the Internet on her research object (www.unil.ch/nt-arabe).
studied undergraduate biochemistry at the University of Glasgow and obtained a PhD in molecular genetics from the University of Lausanne in 1987. After post-doctoral research on signal transduction and cell biology in the yeast Saccharomyces cerevisiae, he joined Novartis AG as a bioinformatics specialist. Continuing in bioinformatics, he returned to academia in 1999 as part of the recently created OIT group of the Ludwig Institute for Cancer Research in Lausanne, and was subsequently appointed Associate Investigator in the LICR Computational Genomics Group. He joined the Vital-IT group as a Senior Scientist in January 2011.
studied computer science at Ecole Polytechnique in France where he obtained his Ingénieur Polytechnicien diploma and master degree in 2007. He received his PhD in bioinformatics (transmembrane proteins structure prediction) from Ecole Polytechnique in 2011. From 2011 to 2013, he did his postdoctoral research at University of Evry, University of Paris Sud and CNRS (France), where he worked on microRNA prediction and RNA-seq data analysis. He joined Vital-IT in January 2014 as a research associate, working with Marco Pagni on genome-scale metabolic networks and RNA-seq data.
has a hybrid background in both medicine (Federal Diploma in Medicine obtained in Geneva back in 2005) and bioinformatics (joint Master in Bioinformatics and Proteomics obtained in Geneva in 2009). Ivan has strong interests in Medical Imaging and in general purpose programming on graphic cards (GPGPU). He joined Vital-IT in January 2013 and currently is in charge of software packaging and deploying on the Vital-IT cluster.
obtaining his Federal Diploma in IGES, administrative data processing, in Neuchâtel. He has being working as a system engineer, network administrator and web developper since 2000. He was involved in various projects like consultant for Nestlé and Orange. In 2010 he graduated in Web Project Management in Lausanne. Since 2011 he is part of the Vital-IT system administration team.
obtained a master's degree in computer science from the University of Basel in 2010. She joined Vital-IT and the Lausanne Genomic Technologies Facility (UNIL) in 2010. She is involved in microarray data analysis for SIB projects and for external clients.
obtained his B.Sc. in Physics from the Technion–Israel Institute of Technology, his M.Sc. in Theoretical Physics and his Ph.D. in Experimental High Energy Physics both from Tel-Aviv University. Worked as a Research associated in Physics at the Weizmann Institute in Rehovot and a Research Physicist at the European Organization for Nuclear Research (CERN) in Geneva. As a Member of the ZEUS Collaboration at DESY, he worked searching for Lepto-Quarks and participated in the construction and installation of the Leading Proton Spectrometer Detector. In the OPAL Collaboration at CERN, he worked in the search for the Higgs Boson and performed high precision measurements of the standard model of fundamental interactions. In the CMS Collaboration he worked in the installation and simulation studies of the CMS Detector, in which the Higgs Boson was discovered in 2012 at CERN. Participated in the development of the first analogical dynamic memory, used in the ZEUS detector, and the construction of Gamma Cameras in Nuclear Medicine. He joined Vital-IT in January 2014 to work in data analysis and reduction, mathematical modeling and optimization, and to support the applications in life and medical sciences.